Fast and Efficient Compression of Floating-Point Data

Large scale scientific simulation codes typically run on a cluster of CPUs that write/read time steps to/from a single file system. As data sets are constantly growing in size, this increasingly leads to I/O bottlenecks. When the rate at which data is produced exceeds the available I/O bandwidth, th...

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Vydané v:IEEE transactions on visualization and computer graphics Ročník 12; číslo 5; s. 1245 - 1250
Hlavní autori: Lindstrom, P., Isenburg, M.
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: United States IEEE 01.09.2006
The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
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ISSN:1077-2626, 1941-0506
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Abstract Large scale scientific simulation codes typically run on a cluster of CPUs that write/read time steps to/from a single file system. As data sets are constantly growing in size, this increasingly leads to I/O bottlenecks. When the rate at which data is produced exceeds the available I/O bandwidth, the simulation stalls and the CPUs are idle. Data compression can alleviate this problem by using some CPU cycles to reduce the amount of data needed to be transfered. Most compression schemes, however, are designed to operate offline and seek to maximize compression, not throughput. Furthermore, they often require quantizing floating-point values onto a uniform integer grid, which disqualifies their use in applications where exact values must be retained. We propose a simple scheme for lossless, online compression of floating-point data that transparently integrates into the I/O of many applications. A plug-in scheme for data-dependent prediction makes our scheme applicable to a wide variety of data used in visualization, such as unstructured meshes, point sets, images, and voxel grids. We achieve state-of-the-art compression rates and speeds, the latter in part due to an improved entropy coder. We demonstrate that this significantly accelerates I/O throughput in real simulation runs. Unlike previous schemes, our method also adapts well to variable-precision floating-point and integer data
AbstractList Large scale scientific simulation codes typically run on a cluster of CPUs that write/read time steps to/from a single file system. As data sets are constantly growing in size, this increasingly leads to I/O bottlenecks. When the rate at which data is produced exceeds the available I/O bandwidth, the simulation stalls and the CPUs are idle. Data compression can alleviate this problem by using some CPU cycles to reduce the amount of data needed to be transfered. Most compression schemes, however, are designed to operate offline and seek to maximize compression, not throughput. Furthermore, they often require quantizing floating-point values onto a uniform integer grid, which disqualifies their use in applications where exact values must be retained. We propose a simple scheme for lossless, online compression of floating-point data that transparently integrates into the I/O of many applications. A plug-in scheme for data-dependent prediction makes our scheme applicable to a wide variety of data used in visualization, such as unstructured meshes, point sets, images, and voxel grids. We achieve state-of-the-art compression rates and speeds, the latter in part due to an improved entropy coder. We demonstrate that this significantly accelerates I/O throughput in real simulation runs. Unlike previous schemes, our method also adapts well to variable-precision floating-point and integer data.Large scale scientific simulation codes typically run on a cluster of CPUs that write/read time steps to/from a single file system. As data sets are constantly growing in size, this increasingly leads to I/O bottlenecks. When the rate at which data is produced exceeds the available I/O bandwidth, the simulation stalls and the CPUs are idle. Data compression can alleviate this problem by using some CPU cycles to reduce the amount of data needed to be transfered. Most compression schemes, however, are designed to operate offline and seek to maximize compression, not throughput. Furthermore, they often require quantizing floating-point values onto a uniform integer grid, which disqualifies their use in applications where exact values must be retained. We propose a simple scheme for lossless, online compression of floating-point data that transparently integrates into the I/O of many applications. A plug-in scheme for data-dependent prediction makes our scheme applicable to a wide variety of data used in visualization, such as unstructured meshes, point sets, images, and voxel grids. We achieve state-of-the-art compression rates and speeds, the latter in part due to an improved entropy coder. We demonstrate that this significantly accelerates I/O throughput in real simulation runs. Unlike previous schemes, our method also adapts well to variable-precision floating-point and integer data.
Large scale scientific simulation codes typically run on a cluster of CPUs that write/read time steps to/from a single file system. As data sets are constantly growing in size, this increasingly leads to I/O bottlenecks. When the rate at which data is produced exceeds the available I/O bandwidth, the simulation stalls and the CPUs are idle. Data compression can alleviate this problem by using some CPU cycles to reduce the amount of data needed to be transfered. Most compression schemes, however, are designed to operate offline and seek to maximize compression, not throughput. Furthermore, they often require quantizing floating-point values onto a uniform integer grid, which disqualifies their use in applications where exact values must be retained. We propose a simple scheme for lossless, online compression of floating-point data that transparently integrates into the I/O of many applications. A plug-in scheme for data-dependent prediction makes our scheme applicable to a wide variety of data used in visualization, such as unstructured meshes, point sets, images, and voxel grids. We achieve state-of-the-art compression rates and speeds, the latter in part due to an improved entropy coder. We demonstrate that this significantly accelerates I/O throughput in real simulation runs. Unlike previous schemes, our method also adapts well to variable-precision floating-point and integer data
A plug-in scheme for data-dependent prediction makes our scheme applicable to a wide variety of data used in visualization, such as unstructured meshes, point sets, images, and voxel grids.
Large scale scientific simulation codes typically run on a cluster of CPUs that write/read time steps to/from a single file system. As data sets are constantly growing in size, this increasingly leads to I/O bottlenecks. When the rate at which data is produced exceeds the available I/O bandwidth, the simulation stalls and the CPUs are idle. Data compression can alleviate this problem by using some CPU cycles to reduce the amount of data needed to be transfered. Most compression schemes, however, are designed to operate offline and seek to maximize compression, not throughput. Furthermore, they often require quantizing floating-point values onto a uniform integer grid, which disqualifies their use in applications where exact values must be retained. We propose a simple scheme for lossless, online compression of floating-point data that transparently integrates into the I/O of many applications. A plug-in scheme for data-dependent prediction makes our scheme applicable to a wide variety of data used in visualization, such as unstructured meshes, point sets, images, and voxel grids. We achieve state-of-the-art compression rates and speeds, the latter in part due to an improved entropy coder. We demonstrate that this significantly accelerates I/O throughput in real simulation runs. Unlike previous schemes, our method also adapts well to variable-precision floating-point and integer data.
Author Lindstrom, P.
Isenburg, M.
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  surname: Isenburg
  fullname: Isenburg, M.
BackLink https://www.ncbi.nlm.nih.gov/pubmed/17080858$$D View this record in MEDLINE/PubMed
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Snippet Large scale scientific simulation codes typically run on a cluster of CPUs that write/read time steps to/from a single file system. As data sets are constantly...
A plug-in scheme for data-dependent prediction makes our scheme applicable to a wide variety of data used in visualization, such as unstructured meshes, point...
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StartPage 1245
SubjectTerms Analytical models
Bandwidth
Central processing units
Compressing
Computer simulation
Data compression
Data visualization
Entropy
fast entropy coding
file compaction for I/O efficiency
File systems
Floating point arithmetic
High throughput
Image coding
Integers
large scale simulation and visualization
Large-scale systems
lossless compression
predictive coding
Predictive models
range coder
Studies
Throughput
Visualization
Title Fast and Efficient Compression of Floating-Point Data
URI https://ieeexplore.ieee.org/document/4015488
https://www.ncbi.nlm.nih.gov/pubmed/17080858
https://www.proquest.com/docview/865235538
https://www.proquest.com/docview/68110697
https://www.proquest.com/docview/896189510
Volume 12
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